Proteolysis is one of the most important biochemical reactions during cheese ripening. Studies on the secondary structure of proteins during ripening would be helpful for characterizing protein changes for assessing cheese quality. Fourier transform infrared spectroscopy (FTIR), with self-deconvolution, second derivative analysis and band curve-fitting, was used to characterize the secondary structure of proteins in Cheddar cheese during ripening. The spectra of the amide I region showed great similarity, while the relative contents of the secondary structures underwent a series of changes. As ripening progressed, the α-helix content decreased and the β-sheet content increased. This structural shift was attributed to the strengthening of hydrogen bonds that resulted from hydrolysis of caseins. In summary, FTIR could provide the basis for rapid characterization of cheese that is undergoing ripening.